The usefulness of genomic prediction in crop and livestock breeding programs has prompted efforts to develop new improved algorithms, such as artificial neural networks gradient tree boosting. However, the performance these algorithms not been compared a systematic manner using wide range datasets models. Using data 18 traits across six plant species with different marker densities training population sizes, we linear non-linear algorithms. First, found that hyperparameter selection was...

Abstract Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis. Defining the control of gene expression in a cell-type-specific and context-dependent manner is critical understanding mechanisms through which variation influences complex traits disease pathobiology. To this end, we performed single-cell RNA sequencing tissue from 66 individuals with fibrosis 48 unaffected donors. Using pseudobulk approach, mapped quantitative trait loci...

The ability to predict traits from genome-wide sequence information (i.e., genomic prediction) has improved our understanding of the genetic basis complex and transformed breeding practices. Transcriptome data may also be useful for prediction. However, it remains unclear how well transcript levels can traits, particularly when are scored at different development stages. Using maize (

The Lyme disease spirochete Borrelia burgdorferi is unique among bacteria in its large number of lipoproteins that are encoded by a small, exceptionally fragmented, and predominantly linear genome. Peripherally anchored either the inner or outer membrane facing periplasm external environment, these assume varied roles. A prominent subset functioning as apparent linchpins enzootic tick-vertebrate infection cycle have been explored vaccine targets. Yet, most B. lipoproteome has remained...

Abstract Background Single-cell RNA sequencing (scRNA-seq) has enabled the unbiased, high-throughput quantification of gene expression specific to cell types and states. With cost scRNA-seq decreasing techniques for sample multiplexing improving, population-scale scRNA-seq, thus single-cell quantitative trait locus (sc-eQTL) mapping, is increasingly feasible. Mapping sc-eQTL provides additional resolution study regulatory role common genetic variants on across a plethora states promises...

Plants respond to wounding stress by changing gene expression patterns and inducing the production of hormones including jasmonic acid. This transcriptional response activates specialized metabolism pathways such as glucosinolate in Arabidopsis thaliana. While regulatory factors sequences controlling a subset wound-response genes are known, it remains unclear how wound is regulated globally. Here, we these responses incorporating putative cis-regulatory elements, known transcription factor...

Abstract Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis (PF). Defining the control of gene expression in a cell-type-specific and context-dependent manner is critical understanding mechanisms through which variation influences complex traits disease pathobiology. To this end, we performed single-cell RNA-sequencing tissue from 67 PF 49 unaffected donors. Employing pseudo-bulk approach, mapped quantitative trait loci (eQTL) across 38...

Plant iron deficiency (−Fe) activates a complex regulatory network that coordinates root Fe uptake and distribution to sink tissues. In Arabidopsis (Arabidopsis thaliana), FER-LIKE FE DEFICIENCY–INDUCED TRANSCRIPTION FACTOR (FIT), basic helix-loop-helix (bHLH) transcription factor (TF), regulates acquisition genes. Many other −Fe-induced genes are FIT independent, instead regulated by bHLH TFs yet unknown TFs. The cis-regulatory code, is, the elements (CREs) their combinations regulate plant...

Motivation: The scope of many Quantitative Trait Loci (QTL) mapping studies has increased to include different cellular and environmental states. However, drawing biologically relevant conclusions from the large, high-dimensional data that come multi-state QTL is not straightforward. Results: To address this problem, we introduce two R packages, QTLExperiment multistateQTL. package provides a robust container for storing manipulating summary statistics associated metadata. Building upon...

Multicellular organisms have diverse cell types with distinct roles in development and responses to the environment. At transcriptional level, differences environmental response between are due regulatory programs. In plants, although cell-type been examined, it is unclear how these regulated. Here, we identify a set of putative cis-regulatory elements (pCREs) enriched promoters genes responsive high-salinity stress six Arabidopsis (

Abstract Plants respond to their environment by dynamically modulating gene expression. A powerful approach for understanding how these responses are regulated is integrate information about cis-regulatory elements (CREs) into models called codes. Transcriptional response combined stress typically not the sum of individual stresses. However, codes underlying have been established. Here we modeled transcriptional single and heat drought in Arabidopsis thaliana. We grouped genes pattern...

Plants are exposed to a variety of environmental conditions, and their ability respond variation depends on the proper regulation gene expression in an organ-, tissue-, cell type-specific manner. Although our knowledge how stress responses regulated is accumulating, genome-wide model plant transcription factors (TFs) cis-regulatory elements control spatially specific response has yet emerge. Using Arabidopsis (Arabidopsis thaliana) as model, we identified set 1,894 putative (pCREs) that...

Transcription factors (TFs) play a key role in regulating plant development and response to environmental stimuli. While most genes revert single copy after whole genome duplication (WGD) event, transcription are retained at significantly higher rate. Little is known about how TF duplicates have diverged their expression regulation, the answer which may contribute better understanding of elevated retention rate among TFs. Here we assessed what features explain differences other using...

Abstract Population-scale single-cell RNA sequencing (scRNA-seq) is now viable, enabling finer resolution functional genomics studies and leading to a rush adapt bulk methods develop new single-cell-specific perform these studies. Simulations are useful for developing, testing, benchmarking but current scRNA-seq simulation frameworks do not simulate population-scale data with genetic effects. Here, we present splatPop, model flexible, reproducible, well-documented of known expression...

Machine learning (ML) has emerged as a critical tool for making sense of the growing amount genetic and genomic data available because its ability to find complex patterns in high dimensional heterogeneous data. While complexity ML models is what makes them powerful, it also difficult interpret. Fortunately, recent efforts develop approaches that make inner workings understandable humans have improved our novel biological insights using ML. Here we discuss importance interpretable ML,...

Abstract The usefulness of Genomic Prediction (GP) in crop and livestock breeding programs has led to efforts develop new improved GP approaches including non-linear algorithm, such as artificial neural networks (ANN) (i.e. deep learning) gradient tree boosting. However, the performance these algorithms not been compared a systematic manner using wide range datasets models. Using data 18 traits across six plant species with different marker densities training population sizes, we linear five...

The origin of sea lamprey ( Petromyzon marinus ) in Lake Champlain has been heavily debated over the past decade. Given lack historical documentation, two competing hypotheses have emerged literature. First, it argued that relatively recent population size increase and concomitant rise wounding rates on prey populations are indicative an invasive entered lake through Canal. Second, genetic evidence suggests a post-glacial colonization at end Pleistocene, approximately 11,000 years ago. One...

Abstract Single-cell RNA-sequencing (scRNA-seq) has enabled the unbiased, high-throughput quantification of gene expression specific to cell types and states. With cost scRNA-seq decreasing techniques for sample multiplexing improving, population-scale scRNA-seq, thus single-cell quantitative trait locus (sc-eQTL) mapping, is increasingly feasible. Mapping sc-eQTL provides additional resolution study regulatory role common genetic variants on across a plethora states, promises improve our...

Abstract The ability to predict traits from genome-wide sequence information (Genomic Prediction, GP), has improved our understanding of the genetic basis complex and transformed breeding practices. Transcriptome data may also be useful for GP. However, it remains unclear how well transcript levels can traits, particularly when are scored at different development stages. Using maize markers seedlings mature plant we found marker models have similar performance. Surprisingly, important...

Abstract Genomic prediction, where genotype information is used to predict phenotypes, has accelerated the breeding processes and can provide mechanistic insights into phenotypes of interest. Switchgrass ( Panicum virgatum L.) a perennial biofuel feedstock with multiple traits targeted for using genomic prediction approaches. To optimize switchgrass we assessed impact genome assembly versions, sequencing strategies variant calling, types, allelic complexities, polyploidy levels on 20 in...

Abstract Extensive transcriptional activity occurring in intergenic regions of genomes has raised the question whether transcription represents novel genes or noisy expression. To address this, we evaluated cross-species and post-duplication sequence expression conservation transcribed (ITRs) four Poaceae species. Among 43,301 ITRs across species, 34,460 (80%) are species-specific. found species tend to be more divergent have recent duplicates compared annotated genes. assess if functional...

Abstract Research on public views of biotechnology has centered genetically modified (GM) foods. However, as the breadth applications grows, a better understanding concerns about non-agricultural products is needed in order to develop proactive strategies address these concerns. Here, we explore perceived benefits and risks associated with five how those perceptions translate into opinion use regulation United States. While found greater support for product, 70% individuals surveyed showed...